get_magma_paths: Get MAGMA Paths

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Get MAGMA Paths

Description

Gets paths to folders based on location of the GWAS summary statistics file. This avoids the GWAS sumstats folder becoming a mess.

Usage

get_magma_paths(
  gwas_sumstats_path = NA,
  upstream_kb = NA,
  downstream_kb = NA,
  output_path = NA
)

Arguments

gwas_sumstats_path	Path to the GWAS summary statistics file.
upstream_kb	How many kb upstream of the gene should SNPs be included?
downstream_kb	How many kb downstream of the gene should SNPs be included?
output_path	If being called from magma_tileplot then gwas_sumstats_path cannot be specified, so instead specificity the base folder where MAGMA_Figures exists.

Value

File path for where MAGMA files should be created

Source

gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas( trait = "educational_attainment") magmaPaths <- MAGMA.Celltyping:::get_magma_paths( gwas_sumstats_path = gwas_sumstats_path, upstream_kb = 35, downstream_kb = 10)

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.